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- PDB-2di7: Solution structure of the filamin domain from human BK158_1 protein -

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Basic information

Entry
Database: PDB / ID: 2di7
TitleSolution structure of the filamin domain from human BK158_1 protein
ComponentsBK158_1
KeywordsSTRUCTURAL PROTEIN / beta-sandwich / immunoglobulin-like fold / filamin domain / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


EGF-domain serine glucosyltransferase activity / EGF-domain serine xylosyltransferase activity / protein O-linked glycosylation via serine / UDP-xylosyltransferase activity / UDP-glucosyltransferase activity / glucosyltransferase activity / Transferases; Glycosyltransferases; Hexosyltransferases / Transferases; Glycosyltransferases; Pentosyltransferases / endomembrane system / endoplasmic reticulum lumen ...EGF-domain serine glucosyltransferase activity / EGF-domain serine xylosyltransferase activity / protein O-linked glycosylation via serine / UDP-xylosyltransferase activity / UDP-glucosyltransferase activity / glucosyltransferase activity / Transferases; Glycosyltransferases; Hexosyltransferases / Transferases; Glycosyltransferases; Pentosyltransferases / endomembrane system / endoplasmic reticulum lumen / nucleoplasm / cytosol
Similarity search - Function
Glycosyl transferase CAP10 domain / : / Glycosyl transferase family 90 / Putative lipopolysaccharide-modifying enzyme. / Filamin/ABP280 repeat / Filamin-type immunoglobulin domains / Filamin/ABP280 repeat / Filamin/ABP280 repeat profile. / Filamin/ABP280 repeat-like / Endoplasmic reticulum targeting sequence. ...Glycosyl transferase CAP10 domain / : / Glycosyl transferase family 90 / Putative lipopolysaccharide-modifying enzyme. / Filamin/ABP280 repeat / Filamin-type immunoglobulin domains / Filamin/ABP280 repeat / Filamin/ABP280 repeat profile. / Filamin/ABP280 repeat-like / Endoplasmic reticulum targeting sequence. / Immunoglobulin E-set / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Protein O-glucosyltransferase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics, restrained molecular dynamics
AuthorsTomizawa, T. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of the filamin domain from human BK158_1 protein
Authors: Tomizawa, T. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S.
History
DepositionMar 29, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 29, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BK158_1


Theoretical massNumber of molelcules
Total (without water)13,5121
Polymers13,5121
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function, structures with the lowest energy, structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein BK158_1


Mass: 13512.179 Da / Num. of mol.: 1 / Fragment: Filamin-type immunoglobulin domains
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Gene: KDELC1 / Plasmid: P050905-05 / Production host: Cell free synthesis / References: UniProt: Q6UW63

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY

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Sample preparation

DetailsContents: 1.11mM Filamin domain U-15N,13C; 20mM d-Tris-HCl(pH 7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 7 / Pressure: ambient / Temperature: 296 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Brukercollection
NMRPipe20030801Delaglio, F.processing
NMRView5.0.4Johnson, B.A.data analysis
KUJIRA0.9742Kobayashi, N.data analysis
CYANA2.0.17Guntert, P.structure solution
CYANA2.0.17Guntert, P.refinement
RefinementMethod: torsion angle dynamics, restrained molecular dynamics
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function, structures with the lowest energy, structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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